VMD-L Mailing List

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Apr 02 2015 - 14:21:15 CDT

It might also be worth noting that TIP3P and TIP4P have the same geometry
for O and H atoms. Presumably VMD/psfgen can handle building the lone pairs
(I've never tried this)? The density of the waterbox may change a little
bit more during equilibration, but I think this is already a "feature" of
equilibration with a TIP3P box.

Brian

On Thu, Apr 2, 2015 at 11:15 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> If you look at the solvate plugin graphical interface, you will
> see that at the bottom of the interface, there is a check box for
> "use nonstandard solvent", and several text fields that you must
> set to provide a small template solvent box, with associated
> PDB, PSF, and topology files, the template box side length, and the
> atom selection that will properly select the template solvent.
> This should described in more detail in the online
> solvate plugin documentation.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Apr 02, 2015 at 06:58:01AM +0000, Kin Leung CHU wrote:
> > I am trying to solvate my system on VMD, but it happens that only
> TIP3P is
> > available readily in VMD with the solvate plugin.
> >
> > In my case, I am somehow required to use the TIP4P water to solvate my
> > system.
> >
> > Is there any easy way to solvate my system using TIP4P water just
> like the
> > solvate plugin does?
> >
> > Thanks a lot.
> >
> > Kelvin Chu
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
> 

-- 
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak_at_uchicago.edu